Is there a quick way to reset a .blend files windows and settings to default
When you open the file there is an option to load the UI from the file which is about to be opened. By default this is enabled, deselecting this option will keep the current settings. See image below.

Edit - Updated with comment by @Samble

In the user preferences under File there is an option for Load UI - this is the default that is used each time you open a file. If it helps you can turn it off and manually turn it on only when you want to load the UI from a file.

Once the file has been loaded it will use the setting pulled from .blend file and to my knowledge there is no "Reset to Factory UI" or "Reset to Start-Up UI" option like you can do for the start-up .blend. 

Should probably be put in as a feature request as I a lot of people share files and doing it by accident is annoying as you lose your current UI and then have to either reload factory setting or your own blend file to get back your UI before re-open the file you want to load.